Interesting thing going on here. I'm sure you're fine to ride with the 3 quarts of capacity added, and I'm far from a Oil-Level-Nazi (close is fine) but its a curious case. Perhaps an extra thorough job of draining it has emptied a little more than the factory assumed in it's calculations? IMO, I wouldn't be against adding a few oz's to get it to read on the stick, and therefore be more 'correct' than any capacity number. Tape an extension of something to the dip stick to see how much below the level it is?

Is it real cold where you're at? Temperature does make a big difference in level on the 1125's, so Johns very involved method should have the oil really, really, hot and at the highest level it could be. Sort of the same answer ^^^ a different way.

On my 1125's I have the habit of cleaning the strainer as well and theres a few oz's trapped in it once you pop it off. Yes its a messy pain, but it's also a great way to check what big things have been caught cycling through the engine. Did you do that? I'm also in the habit of cutting the filter apart because it's so easy to do on them.

I'd be very interested to see whats going on. I have a couple 1125's and 2 1125 engines around here currently if you need me to compare anything for you, let me know.